Darrell Koskinen wrote:
Hi Mark,
I did not have the statement "periodic_molecules = yes" in the .mdp
files. I only had the statement "pbc=xyz" in the .mdp files.
So, I added the "periodic_molecules = yes" statement to the .mdp files
and ran the simulation again. However, this did not appear to resolve
the problem as I received the same warning.
Well that's a pretty basic requirement that you needed to satisfy.
Obviously you also need to re-generate your .tpr from the new .mdp.
That'd be the most likely reason for an *identical* output.
Have you done enough background reading (e.g. wiki page on Carbon
Nanotube simulations) and/or gotten some experience with normal GROMACS
simulations?
Mark
Date: Mon, 21 Sep 2009 16:56:48 +1000
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4ab723b0.6040...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Darrell Koskinen wrote:
Dear GROMACS-ians,
I have created an infinite graphene sheet and upon running grompp, I
get the following response:
/Warning: 1-4 interaction between 10085 and 10445 at distance 19.679
which is larger than the 1-4 table size 1.000 nm
Warning: 1-4 interaction between 9244 and 9963 at distance 19.553
which is larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
These are ignored for the rest of the simulation/
I assume that atoms from opposite ends of the simulation box are
being seen by GROMACS as being 1-4 neighbors as a result of the PBC,
but the shortest distance between the atoms is not being observed. Is
this the problem? Is this problem resulting in the system exploding?
And, how do I resolve this problem?
Did you use periodic_molecules = yes in your .mdp file?
Mark
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